Cultivating Coexistence – “Chaos” Substrate

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CannedGoods
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby CannedGoods » Mon Mar 13, 2017 6:57 am

Noughtypixy wrote:I have been spotting for an organism that only reproduces more of itself then copying it to look at genome then setting 1 as initial and comparing the first splits with the same from an organism I think is different to see if it actually is or is just a different section of the genome.]


Thanks for sharing this technique Noughtypixy. I've done this too. Sometimes I will save each potential orgasm from the microscope and take it to a sterile substrate and make sure they are all separate species.

It's a little annoying that COLOR is not a mutation that seems to happen very often. Although, I've noticed that color does change if you put on "point mutations only," but it can still be a slow process. I've thought about allowing people to modify the color of the species if for no other reason than to act as a dye so you can tell different kinds apart more easily.

Noughtypixy wrote:....phagodippers and duophotes...
:)

Thanks for sharing! Nice colors on this one!

Noughtypixy wrote:this little beauty is the photoworm...
:o

Thanks for sharing this one too! Really awesome start. I inserted it a few times and got it to evolve into something really fun Again... the spirit of this is more of an artistic exploration of all the potential things that can emerge in this substrate than trying to technically beat the challenge. As long as we are allowing the mechanics to evolve without editing the genome directly, I think it is OK to save some really interesting proto-species that may not quite have what it takes to survive from the beginning without going extinct and re-insert it until it finds a mutation that works. Just maybe mention that it is a "rescue."

CannedGoods
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby CannedGoods » Mon Mar 13, 2017 8:33 am

bwisialo wrote:I'm guessing you saw the True Evolution Challenge. I've tried it, but by developing solutions from contaminated cells on a challenge by challenge basis, without the solutions having a common ancestor.


Were you actually you complete all the challenges this way?

I did see that, and I've tried to do this. I've had some success but trying to figure out what the challenge substrates are set to is a challenge all it's own.

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bwisialo
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby bwisialo » Mon Mar 13, 2017 9:07 am

Oh, not even close. :lol: I completed the same challenges as chargrill plus a couple more. All Algae challenges; Macro 1-3; Decimation, Conquering, both Sun challenges. Others should be doable: Macro 4-5; Countermeasure with a lot of effort; Floaters, perhsps both Slippery slope. Yeah, reconstructing the substrates is quite difficult for many of the challenges.
amor fati

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Re: Cultivating Coexistence – “Chaos” Substrate

Postby CannedGoods » Mon Mar 13, 2017 3:22 pm

@ wacaplet
Thanks for all the great feedback and detailed documentation about your findings. I like the way you approach this challenge. Points for fun names too. ;) You seem to have found the spirit of this challenge. You can take ALL the liberties with the rules. :D

I think there is a lot of room to be creative with alternate and/or additional rules for challenges like this, even other substrates to explore in this manner.

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wapcaplet
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby wapcaplet » Tue Mar 14, 2017 2:58 am

I ran evolution overnight (for over 200,000 substrate hours) and got an astonishingly complicated multi-swimmer genome, plus a rather simple devorocyte parasite that feeds on them:

chaos-shape-shifter-and-spiky.substrate
shape-shifter-and-spiky.png


I changed their colors to make them easier to distinguish. The black one is "spiky", and the multi-colored one is "shape shifter". Shape shifter uses 16 modes in its genome, with 8 phagocyte modes, 6 devorocyte modes, and 2 flagellocyte modes appearing during its reproductive cycle. Pairs of phagocytes become pairs of devorocytes which become pairs of swimmers. There are red and purple swimmers, with two different kinds of purple swimmer. They change forms rapidly; all the devorocyte modes split immediately and do not have much time to feed on other cells.

Here is the full genome, as I mapped it out in shorthand. This is each used mode number, type (p/f/d), and the mode numbers of its two children:

1p-16+13
2f-20+7
3p-14+14
4p-7+8
6d-13+7
7p-11+19
8p-12+20
9f-8+20
10p-3+8
11d-19+19
12d-14+2
13p-6+6
14p-1+1
16d-7+7
19d-4+9
20d-10+2

Some points of interest: Twins are somewhat common. Modes 3, 11, 13, 14, and 16 all make two of the same modes as their children (twins). This is the "peanut" phenomenon I noted above; there seems to be a tendency for phagocyte or photocyte twins to appear in many genomes I've evolved on this substrate. There are several cycles within the genome (2/20, 4/7/19, 8/20/10, etc.) that probably help its reproductive success; there's more than one way to create most of the modes. Its short-lived devorocyte phase is intriguing. Why use devorocytes here? What advantage did it provide that made it keep them over 200,000h of evolution? This mechanism is worth exploring more.

Next, I did another "cheat" and turned off the "Substrate with nitrates" checkbox. I wanted to try to evolve both photocyte-based and phagocyte-based organisms with nitrocytes. The photocytes were fairly easy to get started, with only photocytes and nitrocytes to start with. The buoycytes were evolved last, bringing them across the top third of substrate.

I evolved the phagocyte-based one separately. With only phagocytes and nitrocytes enabled, it took many attempts and re-contaminations. When I got a genome that expressed both mode types, I loaded it and re-seeded it repeatedly until radiation took hold and made it reproduce. Here is both of them living together, "buoyphode" and "nitrobomb":

chaos-nitrobomb-and-buoyphode.substrate
buoyphode-and-nitrobomb.png
buoyphode-and-nitrobomb.png (48.57 KiB) Viewed 1460 times

CannedGoods
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby CannedGoods » Tue Mar 14, 2017 8:08 am

wapcaplet wrote:I ran evolution overnight (for over 200,000 substrate hours) and got an astonishingly complicated multi-swimmer genome, plus a rather simple devorocyte parasite that feeds on them:

I changed their colors to make them easier to distinguish. The black one is "spiky", and the multi-colored one is "shape shifter". Shape shifter uses 16 modes in its genome....


Really cool Wapcaplet! I was actually thinking of a version of this game where the goal is to have the radiation level fixed at a value above zero and then to see who get their randomly generated species to run the longest without going extinct at a medium level radiation.

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bwisialo
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby bwisialo » Tue Mar 14, 2017 8:37 am

I like the Nitrobomb! :)

The twin phenomenon might somehow be a result of the mutation that duplicates one mode in another. I'd have to think about the dynamics more.

I'd be interested to see if the cell type shifts and cycles in fact improve reproductive success. It's often the case that, by over modes, shortcutting cycles produced by evolution improves things.

The short lifespan of the Devorocytes probably balances a benefit to the Devorocytes and the other cells. They live long enough to get some energy, and if the Devorocytes lived longer they would destroy to many and deplete too much from other cells.

Having genomes survive at high radiation isn't difficult if the organism has an easy time reproducing: like Photocytes in static light, or a basic swimmer on a Default plate. That is, it would be a challenge only if it was difficult to get an organism to survive in the first place.
amor fati

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wapcaplet
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby wapcaplet » Wed Mar 15, 2017 2:12 am

Feeling bored with photocytes, I tried exploring phagocyte-based organisms. A simple phagocyte-only genome can get by on this substrate, but the density gradient leaves a lot of unexplored territory, since normal cells can't reach the very bottom, and seldom reach the very top. But if they could include buoyocytes... So, I seeded with only phagocytes and buoyocytes. With some patience, a few "light" or "heavy" cell clusters began to form. Without adding any other cell types, I got a range of curious and complex results.

Here is the lineage of Booeys. First, an early version, producing sinking strings of adhesined phagocytes.

chaos booey 1.substrate

With some light radiation and a few minutes of incubation, this weird mutation happened--mode M2 (yellow) makes M2+M2 in a fractal pattern, and one other mode in the genome sometimes makes an M2:

chaos booey 2.substrate
booey-2.png


A couple more variations:

chaos booey 3.substrate
chaos booey 4.substrate

I added some color-coding to one of the intermediate genomes. This one has two buoyocytes. Red is low density, blue is high density. Both of them are frequently attached to one or more phagocytes, or to each other. Being able to both float and sink allows the organism to claim more of the food on the substrate.

chaos bipolar booeys.substrate
bipolar-booey.png


The latest, most "evolved", has multiple buoyocytes attached to one or two phagocytes. This lets them sink all the way to the bottom, or float all the way to the top, or just about anywhere in between.

chaos booey 5.substrate
booey-5.png
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CannedGoods
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby CannedGoods » Fri Oct 06, 2017 7:22 pm

So... I took this challenge, and I made it into an interactive thing with props and an LED projector that the average person can walk up to an interact with, with a little coaching.

I'm doing this for FREE (actually, at my own expense) just to share this fun thing I like to do with Cell Lab with the public.

Pictures and video of the set-up coming soon.

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121daredevil
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Re: Cultivating Coexistence – “Chaos” Substrate

Postby 121daredevil » Sat Oct 07, 2017 1:39 am

Wow! I am Appreciated i will try it!
For every failure has made. Try and try again and Success will be achieved

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